3-101978364-A-G

Variant names:

• chr3-101978364-A-G
• rs1514471
• ENST00000483840.1:n.106-16197A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000483840.1(ENSG00000241280):​n.106-16197A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 151,856 control chromosomes in the GnomAD database, including 7,466 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.31 (7466 hom., cov: 31)
• Consequence: ENSG00000241280 ENST00000483840.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350

Genes affected

ENSG00000241280 (HGNC:):

RDUR (HGNC:27190): (RIG-I dependent antiviral response regulator RNA)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RDUR	NR_026934.1	n.269-16197A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000241280	ENST00000483840.1	n.106-16197A>G		intron_variant	Intron 1 of 2	1
ENSG00000241280	ENST00000498624.1	n.347-16197A>G		intron_variant	Intron 1 of 2	1
RDUR	ENST00000465215.1	n.269-16197A>G		intron_variant	Intron 2 of 3	2

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47088 AN: 151736 Hom.: 7463 Cov.: 31

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.337

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.310 AC: 47118 AN: 151856 Hom.: 7466 Cov.: 31 AF XY: 0.305 AC XY: 22618 AN XY: 74180

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.469

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.338

Alfa AF: 0.341 Hom.: 18280

Bravo AF: 0.316

Asia WGS AF: 0.319 AC: 1107 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.58

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1514471; hg19: chr3-101697208;